Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001315.1 Hibiscus syriacus cultivar Beakdansim tig00002563_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 79471
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:304 original size:17 final size:17
Alignment explanation
Indices: 284--316 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
274 ACAAAAAGGG
284 CAAAAAACAAAAAAAAA
1 CAAAAAACAAAAAAAAA
301 CAAAAAACAAAAAAAA
1 CAAAAAACAAAAAAAA
317 GAAAGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (17 bp):
CAAAAAACAAAAAAAAA
Found at i:990 original size:22 final size:22
Alignment explanation
Indices: 937--991 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
927 AGCACCCCAT
*
937 CAAACCTTTAAGAATCAAATGC
1 CAAACCTTTGAGAATCAAATGC
*
959 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGAATCAAATGC
981 CAAACCTTTGA
1 CAAACCTTTGA
992 CCAACACAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGAATCAAATGC
Found at i:2134 original size:104 final size:105
Alignment explanation
Indices: 1903--3672 Score: 2382
Period size: 104 Copynumber: 17.1 Consensus size: 105
1893 TGGCCATCCG
* * * * * * *
1903 CAATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACG
1 CAATTTCAACTTCACAACGAAGGATAT--TG-GACTCCAGACAACGCAAGTTCAACTTCACGACG
* * * *
1968 AA-GGA-TGACTGGTT-TCAACAAACACTTCCCAAATTCATAGC
63 AAGGGACCG-CTGGTTGTCAACAAACAATTCCCAATTTCAGAGC
* * * ** *
2009 C-ATTTCAACTTCATAGCGAAGGATATTGGACTCCAGAAAATACAAGTTCAACTTCAC-ACAAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
2072 GGACCGCTGGTTCTCAATAAATAACTT-CCAATTTTAGAGC
66 GGACCGCTGGTTGTCAACAAACAA-TTCCCAATTTCAGAGC
*
2112 CAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC-AAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
2176 GGACCGCTGGTTGTCAATAATA-ATTTCTCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAA-ACAATTCCCAATTTCAGAGC
*
2216 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
2281 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAA-TTCCCAATTTCAGAGC
* * * *
2322 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGTCAACGCAAGTTCAACTTCACGAAGAA-
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
2386 GGACCGCTGGTTGTCAACAAACAATTCTCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGC
*
2426 CAATTTCAACTT--C-AC-AAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
2487 GGACTGCTGATTATCAATAAACAACTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAA-TTCCCAATTTCAGAGC
* * *
2528 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
** *
2593 GGATTGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGC
66 GGACCGCTGGTTGTCAACAAACAA-TTCCCAATTTCAGAGC
*
2634 CAATTTCAACTTCACAACGAA-GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
2698 GGA-CGCTGGTTATCAACAAACAATTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGC
* * *
2737 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
2802 GGACCGTTGGTTGTCAACAAATAATTCTCAATTTC-GAGC
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGC
* *
2841 CAATTTCAACTTCAC-ACGAA-GATATTGGACTCCAGTCAACGCAAGTTCAACTTCACGAAGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
2904 GGACCGCTGGTTGTCAACAAAC--TTCCCAATTTC-G-GC
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGC
*
2940 CAATTTCAACTTCACAGCGAAGGATATT-GACTCCA-ACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
3003 GGACCGTTGGTTATCAA-AAA-ACTTCTCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGC
*
3041 CAATTTCAACTTCACAGCGAAGGATATT-GACTCCAGACAACGCAAGTTCAACTTCACGA-GAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
3104 GGACCGCTGGTTGTCAACAAACAATT-TC--TTT-TGAGC
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGC
*
3140 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA-AACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
3204 GGACCGCTGGTTGTCAACAAAC-ATTCCCAATTTCGGAGC
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGC
* *
3243 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGA-ACAA-GCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
3306 GGA---TTGGTTGTCAACAAA-ACTTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACA-ATTCCCAATTTCAGAGC
* *
3343 CAATTTCAACTTCACAACGAAAGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
3408 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTC-GAGC
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGC
* * *
3447 CAATTTCAATTTCACAACGAAGGATTTTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
**
3512 GGACCGCTGGTTGTCAACAAACAATTTCCCAATTTTGGAGC
66 GGACCGCTGGTTGTCAACAAACAA-TTCCCAATTTCAGAGC
* * * * * *
3553 CAA-TTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACATGTTCAACTTCACAATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
3617 GGACGGCTGGTTGTCAACAAACAATTTCCCGATTCCAAAGC
66 GGACCGCTGGTTGTCAACAAACAA-TTCCCAATTTCAGAGC
3658 CAATTTCAACTTCAC
1 CAATTTCAACTTCAC
3673 GACGGAGTAT
Statistics
Matches: 1500, Mismatches: 118, Indels: 92
0.88 0.07 0.05
Matches are distributed among these distances:
98 3 0.00
99 137 0.09
100 151 0.10
101 91 0.06
102 205 0.14
103 106 0.07
104 345 0.23
105 268 0.18
106 194 0.13
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGC
Found at i:2547 original size:206 final size:208
Alignment explanation
Indices: 1903--3685 Score: 2216
Period size: 206 Copynumber: 8.6 Consensus size: 208
1893 TGGCCATCCG
* * * * * *
1903 CAATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCAC-AAC
1 CAATTTCAACTTCACAACGAAGGATAT--TG-GACTCAAGACAACGCAAGTTCAACTTCACGAA-
* * * *
1967 GAA-GGA-TGACTGGTT-TCAACAAACACTTCCCAAATTCATAGCC-ATTTCAACTTCATAGCGA
62 GAAGGGACCG-CTGGTTGTCAACAAACAATTCCCAATTTCAGAGCCAATTTCAACTTC--A-CGA
* ** * * *
2028 AGGATATTGGACTCCAGAAAATACAAGTTCAACTTCAC-ACAAAGGGACCGCTGGTTCTCAATAA
123 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* *
2092 ATAACTT-CCAATTTTAGAGC
188 ACAACTTCCCAATTTCAGAGC
* * *
2112 CAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG-ACAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAGAAG
* * *
2176 GGACCGCTGGTTGTCAATAATA-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
66 GGACCGCTGGTTGTCAACAA-ACAATTCCCAATTTCAGAGCCAATTTCAACTT--C-ACGAAGGA
* *
2240 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAATAAACAA
127 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA
*
2305 TTTCCCAATTTCAGAGC
192 CTTCCCAATTTCAGAGC
* *
2322 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGTCAACGCAAGTTCAACTTCACGAAGAA-
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAGAAG
*
2386 GGACCGCTGGTTGTCAACAAACAATTCTCAATTTCAGAGCCAATTTCAACTTCAC-AAGGATATT
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGCCAATTTCAACTTCACGAAGGATATT
* * * * *
2450 GGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACTGCTGATTATCAATAAACAACTTC
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
2515 CCAATTTCAGAGC
196 CCAATTTCAGAGC
* * * *
2528 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAGAAG
** *
2593 GGATTGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCAC-AACGAAGA
66 GGACCGCTGGTTGTCAACAAACAA-TTCCCAATTTCAGAGCCAATTTCAACTTCACGAA-G--GA
* *
2657 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGA-CGCTGGTTATCAACAAACAA
127 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA
2721 -TTCCCAATTTCAGAGC
192 CTTCCCAATTTCAGAGC
* *
2737 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA-ACAACGCAAGTTCAACTTCACGATGAA
1 CAATTTCAACTTCACAACGAAGGATATTGGACT-CAAGACAACGCAAGTTCAACTTCACGAAGAA
* * *
2801 GGGACCGTTGGTTGTCAACAAATAATTCTCAATTTC-GAGCCAATTTCAACTTCACACGAA-GAT
65 GGGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGCCAATTTCAACTT--CACGAAGGAT
* *
2864 ATTGGACTCCAGTCAACGCAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAAC--A-AAC
128 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
2926 TTCCCAATTTC-G-GC
193 TTCCCAATTTCAGAGC
* * *
2940 CAATTTCAACTTCACAGCGAAGGATATT-GACTCCA-ACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAGAAG
* * * *
3003 GGACCGTTGGTTATCAA-AAA-ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGCCAATTTCAACTT--CA-CGAAGGAT
3066 ATT-GACTCCAGACAACGCAAGTTCAACTTCACGA-GAAGGGACCGCTGGTTGTCAACAAACAA-
128 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
* *
3128 TT-TC--TTT-TGAGC
193 TTCCCAATTTCAGAGC
* *
3140 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA-AACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAGAAG
*
3204 GGACCGCTGGTTGTCAACAAAC-ATTCCCAATTTCGGAGCCAATTTCAACTTCACAGCGAAGGAT
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGCCAATTTCAACTT--CA-CGAAGGAT
* *
3268 ATTGGACTCGA-ACAA-GCAAGTTCAACTTCACGACGAAGGGA---TTGGTTGTCAAC-AA-AAC
128 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
3326 TTTCCCAATTTCAGAGC
193 -TTCCCAATTTCAGAGC
* * *
3343 CAATTTCAACTTCACAACGAAAGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAGAAG
*
3408 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTC-GAGCCAATTTCAATTTCACAACGAAGGAT
66 GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGCCAATTTCAACTT--C-ACGAAGGAT
* * *
3472 TTTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAT
128 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
**
3537 TTCCCAATTTTGGAGC
193 TTCCCAATTTCAGAGC
* * * *
3553 CAA-TTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACATGTTCAACTTCAC-AATGAA
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAA-GAA
* * * * *
3616 GGGACGGCTGGTTGTCAACAAACAATTTCCCGATTCCAAAGCCAATTTCAACTTCACGACGGAGT
65 GGGACCGCTGGTTGTCAACAAACAA-TTCCCAATTTCAGAGCCAATTTCAACTTCACGAAGGA-T
3681 ATTGG
128 ATTGG
3686 GCTCGAAACA
Statistics
Matches: 1417, Mismatches: 100, Indels: 114
0.87 0.06 0.07
Matches are distributed among these distances:
197 2 0.00
198 2 0.00
199 29 0.02
200 75 0.05
201 145 0.10
202 73 0.05
203 78 0.06
204 86 0.06
205 31 0.02
206 247 0.17
207 77 0.05
208 99 0.07
209 245 0.17
210 165 0.12
211 63 0.04
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (208 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAGAAG
GGACCGCTGGTTGTCAACAAACAATTCCCAATTTCAGAGCCAATTTCAACTTCACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
CCAATTTCAGAGC
Found at i:4489 original size:37 final size:37
Alignment explanation
Indices: 4432--4536 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
4422 ACTTTTTGTC
*
4432 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
4469 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
4506 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
4537 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:5245 original size:19 final size:19
Alignment explanation
Indices: 5201--5257 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
5191 TACTATTTAG
* *
5201 TATTTTATTATA-TTATACA
1 TATTTT-TTATATTTTTATA
5220 TACTTTTTTATATTTTTATA
1 TA-TTTTTTATATTTTTATA
* *
5240 TATTTTTTTTTTTTTTAT
1 TATTTTTTATATTTTTAT
5258 TTTATACTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 21 0.66
20 11 0.34
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTTTATATTTTTATA
Found at i:5250 original size:24 final size:26
Alignment explanation
Indices: 5223--5278 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
5213 TTATACATAC
5223 TTTTTTATATTTTTATA-TATTT-TTT
1 TTTTTTATA-TTTTATACTATTTATTT
*
5248 TTTTTTTTATTTTATACTATTTATTT
1 TTTTTTATATTTTATACTATTTATTT
*
5274 ATTTT
1 TTTTT
5279 CATTATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 7 0.26
25 13 0.48
26 7 0.26
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTTTATATTTTATACTATTTATTT
Found at i:5394 original size:24 final size:24
Alignment explanation
Indices: 5367--5442 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
5357 TATATATATA
5367 TATTTTTCTTCATTTATTTTATTT
1 TATTTTTCTTCATTTATTTTATTT
** *
5391 TATTCAAT-TTCATTT-TTTTATAT
1 TATT-TTTCTTCATTTATTTTATTT
* *
5414 T-TGTTTCTTCCAATTATTTTATGTT
1 TATTTTTCTT-CATTTATTTTAT-TT
5439 TATT
1 TATT
5443 ATTATTGGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 10
0.66 0.16 0.18
Matches are distributed among these distances:
21 1 0.03
22 3 0.08
23 12 0.32
24 17 0.46
25 3 0.08
26 1 0.03
ACGTcount: A:0.20, C:0.09, G:0.03, T:0.68
Consensus pattern (24 bp):
TATTTTTCTTCATTTATTTTATTT
Found at i:6987 original size:46 final size:46
Alignment explanation
Indices: 6934--7024 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
6924 TCAGTGCCAC
* *
6934 ACTAATAATTGTATTATACTACATTCATTCACGAAAACATATTCTA
1 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCTA
6980 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCT
1 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCT
7025 GAACGCTGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (46 bp):
ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCTA
Found at i:7103 original size:74 final size:74
Alignment explanation
Indices: 6980--7147 Score: 291
Period size: 74 Copynumber: 2.3 Consensus size: 74
6970 ACATATTCTA
*
6980 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCTGAACGCTGAGCTTAAGAGCT
1 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCCGAACGCTGAGCTTAAGAGCT
*
7045 CAGTGTCAC
66 CAGTGACAC
* *
7054 ACTAATAACTATATTATACTACATTCATTCACGAAAACATATTCCGAACGCTGAGCTTAAGAGCT
1 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCCGAACGCTGAGCTTAAGAGCT
*
7119 CAGTGACAT
66 CAGTGACAC
7128 ACTAATAACTGTACTATACT
1 ACTAATAACTGTACTATACT
7148 GATATAAAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 87 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (74 bp):
ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCCGAACGCTGAGCTTAAGAGCT
CAGTGACAC
Found at i:11801 original size:16 final size:16
Alignment explanation
Indices: 11776--11812 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
11766 AATAAGTCCT
*
11776 ATTTATTTTATAAATG
1 ATTTAATTTATAAATG
11792 ATTTAATTTATAAATG
1 ATTTAATTTATAAATG
11808 ATTTA
1 ATTTA
11813 TATGATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
ATTTAATTTATAAATG
Found at i:11956 original size:162 final size:162
Alignment explanation
Indices: 11653--11957 Score: 540
Period size: 162 Copynumber: 1.9 Consensus size: 162
11643 GGTGCAGGTT
11653 TGATTTTTATATTTTACAGTAAAGTTCTATTTACAAAGTTTGATTTAATACAACGTGATTTATAG
1 TGATTTTTATATTTTACAGTAAAGTTCTATTTACAAAGTTTGATTTAATACAACGTGATTTATAG
* * *
11718 ACTAAAGATTAAAAGTTAATTGCATATGAAATATATGAAAATGATTTTAATAAGTCCTATTTATT
66 ACGAAAGATTAAAAGTTAATCGCATATGAAATATATGAAAATGATTTTAACAAGTCCTATTTATT
11783 TTATAAATGATTTAATTTATAAATGATTTATA
131 TTATAAATGATTTAATTTATAAATGATTTATA
*
11815 TGATATTTTATATTTTATAGTAAAGTTCTATTTACAAAGTTTGATTTAATACAACGTGATTTATA
1 TGAT-TTTTATATTTTACAGTAAAGTTCTATTTACAAAGTTTGATTTAATACAACGTGATTTATA
* *
11880 GACGAAATATT-AAAGTTAATCGTATATGAAATATATGAAAATGATTTTAACAAGTCCTATTTAT
65 GACGAAAGATTAAAAGTTAATCGCATATGAAATATATGAAAATGATTTTAACAAGTCCTATTTAT
11944 TTTATAAATGATTT
130 TTTATAAATGATTT
11958 TATATGATAT
Statistics
Matches: 136, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
162 68 0.50
163 68 0.50
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.44
Consensus pattern (162 bp):
TGATTTTTATATTTTACAGTAAAGTTCTATTTACAAAGTTTGATTTAATACAACGTGATTTATAG
ACGAAAGATTAAAAGTTAATCGCATATGAAATATATGAAAATGATTTTAACAAGTCCTATTTATT
TTATAAATGATTTAATTTATAAATGATTTATA
Found at i:19279 original size:85 final size:85
Alignment explanation
Indices: 19143--19305 Score: 263
Period size: 85 Copynumber: 1.9 Consensus size: 85
19133 TTTAATTGTG
* ** *
19143 GTTTTTTTACAGGCGTGGGAAAATCATGTTTGCTCTTGCAGTTTATTGACAAGAGATTCCAATCG
1 GTTTTTTTACAGGCGTGGAAAAATCATGTTTGCTCTTGCAGTTTACCGACAAGAGATTCCAACCG
* *
19208 GTTCATGATTTAATCGGCGA
66 ATTCAAGATTTAATCGGCGA
*
19228 GTTTTTTTACAGGCGTGGAAAAATCATGTTTGCTCTTGCATTTTACCGACAAGAGATTCCAACCG
1 GTTTTTTTACAGGCGTGGAAAAATCATGTTTGCTCTTGCAGTTTACCGACAAGAGATTCCAACCG
19293 ATTCAAGATTTAA
66 ATTCAAGATTTAA
19306 CCATCGGTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (85 bp):
GTTTTTTTACAGGCGTGGAAAAATCATGTTTGCTCTTGCAGTTTACCGACAAGAGATTCCAACCG
ATTCAAGATTTAATCGGCGA
Found at i:21438 original size:43 final size:43
Alignment explanation
Indices: 21391--21472 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
21381 ACAAAATGTT
*
21391 GCTATATGTCGCGACCTTTTGC-GATGTTTGTTCCTAAAATGCC
1 GCTATATGTCGCGACCTTTTGCAGA-GTTTATTCCTAAAATGCC
*
21434 GCTATATGTCTCGACCTTTTGCAGAGTTTATTCCTAAAA
1 GCTATATGTCGCGACCTTTTGCAGAGTTTATTCCTAAAA
21473 CACTGTTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 34 0.94
44 2 0.06
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (43 bp):
GCTATATGTCGCGACCTTTTGCAGAGTTTATTCCTAAAATGCC
Found at i:27403 original size:13 final size:12
Alignment explanation
Indices: 27385--27453 Score: 56
Period size: 13 Copynumber: 5.6 Consensus size: 12
27375 TCACAACCTG
27385 ACCCGACCCGTTT
1 ACCCGACCCG-TT
27398 ACCCGACCCG--
1 ACCCGACCCGTT
27408 ACCCGTTTACCCG--
1 ACCCG---ACCCGTT
27421 ACCCGACCCGTTT
1 ACCCGACCCG-TT
27434 ACCCGACCCGTT
1 ACCCGACCCGTT
27446 GACCCGAC
1 -ACCCGAC
27454 TCGACCCGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.20
12 2 0.04
13 37 0.76
ACGTcount: A:0.17, C:0.49, G:0.17, T:0.16
Consensus pattern (12 bp):
ACCCGACCCGTT
Found at i:27438 original size:31 final size:31
Alignment explanation
Indices: 27403--27482 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
27393 CGTTTACCCG
*
27403 ACCCGACCCGTTTACCCGACCCGACCCGTTT
1 ACCCGACCCGTTGACCCGACCCGACCCGTTT
* *
27434 ACCCGACCCGTTGACCCGACTCGACCCGTTG
1 ACCCGACCCGTTGACCCGACCCGACCCGTTT
*
27465 ACCGTTGACCCGTTGACC
1 ACC--CGACCCGTTGACC
27483 GTTGACCGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 31 0.72
33 12 0.28
ACGTcount: A:0.16, C:0.45, G:0.20, T:0.19
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGACCCGTTT
Found at i:27467 original size:18 final size:18
Alignment explanation
Indices: 27384--27443 Score: 120
Period size: 18 Copynumber: 3.3 Consensus size: 18
27374 GTCACAACCT
27384 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTTACCC
27402 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTTACCC
27420 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTTACCC
27438 GACCCG
1 GACCCG
27444 TTGACCCGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.17, C:0.50, G:0.18, T:0.15
Consensus pattern (18 bp):
GACCCGACCCGTTTACCC
Found at i:27471 original size:7 final size:7
Alignment explanation
Indices: 27459--27490 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
27449 CCGACTCGAC
27459 CCGTTGA
1 CCGTTGA
27466 CCGTTGA
1 CCGTTGA
27473 CCCGTTGA
1 -CCGTTGA
27481 CCGTTGA
1 CCGTTGA
27488 CCG
1 CCG
27491 GCGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:27476 original size:15 final size:15
Alignment explanation
Indices: 27456--27499 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 15
27446 GACCCGACTC
27456 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
27471 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
27486 GACCGGCGTTGACC
1 GACC--CGTTGACC
27500 ACTGTTGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 19 0.70
17 8 0.30
ACGTcount: A:0.14, C:0.34, G:0.30, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:30016 original size:24 final size:24
Alignment explanation
Indices: 29989--30083 Score: 127
Period size: 24 Copynumber: 4.0 Consensus size: 24
29979 ATTTCCGACT
**
29989 TGAATTCTGTTCTGATAAATGATC
1 TGAATTCTGTTCTGATATCTGATC
*
30013 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
30037 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
30061 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
30084 ATCTTCGTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:30026 original size:12 final size:12
Alignment explanation
Indices: 29989--30081 Score: 82
Period size: 12 Copynumber: 7.8 Consensus size: 12
29979 ATTTCCGACT
29989 TGAATTCTGTTC
1 TGAATTCTGTTC
** *
30001 TG-ATAAATGATC
1 TGAAT-TCTGTTC
30013 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
30025 TGATTTCTGATC
1 TGAATTCTGTTC
*
30037 TGGATTCTGTTC
1 TGAATTCTGTTC
30049 TG-ATATCTGTTC
1 TGAAT-TCTGTTC
*
30061 TGAATTCTGTTT
1 TGAATTCTGTTC
*
30073 TGATTTCTG
1 TGAATTCTG
30082 ATATCTTCGT
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
11 4 0.06
12 56 0.88
13 4 0.06
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.49
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:30080 original size:48 final size:48
Alignment explanation
Indices: 29975--30083 Score: 148
Period size: 48 Copynumber: 2.3 Consensus size: 48
29965 AAATATTTTA
* *
29975 TCTGATTTCCGA-CTTGAATTCTGTTCTGATAAATGATCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTCTGATAAATGATCTGAATTCTGT
** *
30023 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATAAATGATCTGAATTCTGT
*
30071 TTTGATTTCTGAT
1 TCTGATTTCTGAT
30084 ATCTTCGTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 53 0.98
49 1 0.02
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATAAATGATCTGAATTCTGT
Found at i:32230 original size:18 final size:18
Alignment explanation
Indices: 32207--32252 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
32197 ACCGGTCACA
*
32207 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCATTT
32225 ACCCGACCCGACCCATTT
1 ACCCGACCCGACCCATTT
32243 ACCCGACCCG
1 ACCCGACCCG
32253 TTGACTTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.52, G:0.15, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCATTT
Found at i:32299 original size:10 final size:8
Alignment explanation
Indices: 32265--32311 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
32255 GACTTGACTC
32265 GACCCGTT
1 GACCCGTT
32273 GA-CCGTT
1 GACCCGTT
32280 GACCCGTT
1 GACCCGTT
32288 GACCGGCGTT
1 GACC--CGTT
32298 GACCACTGTT
1 GACC-C-GTT
32308 GACC
1 GACC
32312 AAAACTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 1 0.03
10 15 0.44
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:34826 original size:12 final size:12
Alignment explanation
Indices: 34811--34880 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
34801 GATAAATGAC
34811 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
34823 CTGATTTCTGAT
1 CTGAATTCTGTT
*
34835 CTGGATTCTGTT
1 CTGAATTCTGTT
34847 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
34859 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
34871 TTGATTTCTG
1 CTGAATTCTG
34881 ATATCTTCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
11 2 0.04
12 45 0.92
13 2 0.04
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:34830 original size:48 final size:48
Alignment explanation
Indices: 34774--34882 Score: 148
Period size: 48 Copynumber: 2.3 Consensus size: 48
34764 AAATATTTTA
34774 TCTGATTTCTGA-CTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGTTCTGATAAATGACCTGAATTCTGT
* ** **
34822 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
*
34870 TTTGATTTCTGAT
1 TCTGATTTCTGAT
34883 ATCTTCGTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 53 0.98
49 1 0.02
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:34842 original size:24 final size:24
Alignment explanation
Indices: 34774--34882 Score: 130
Period size: 24 Copynumber: 4.5 Consensus size: 24
34764 AAATATTTTA
34774 TCTGATTTCTGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
*** *
34798 TCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
34822 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
34846 TCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
34870 TTTGATTTCTGAT
1 TCTGATTTCTGAT
34883 ATCTTCGTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
24 69 0.99
25 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.49
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:36245 original size:24 final size:24
Alignment explanation
Indices: 36201--36246 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
36191 TTGATGAATA
*
36201 ATATTATATTTATAGATAAATTTT
1 ATATTATATTTATAAATAAATTTT
*
36225 ATATTATGTTT-TAAATGAAATT
1 ATATTATATTTATAAAT-AAATT
36247 AATTGTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (24 bp):
ATATTATATTTATAAATAAATTTT
Found at i:39699 original size:2 final size:2
Alignment explanation
Indices: 39687--39726 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
39677 TAAATTTCCG
*
39687 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39727 TTAAAAGGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40339 original size:23 final size:23
Alignment explanation
Indices: 40313--40366 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
40303 TTGGTGCTCG
*
40313 ACTCATTGCTCGTTAAACTCGTT
1 ACTCATTACTCGTTAAACTCGTT
40336 ACTCATTACTCGTTAAACTCGTT
1 ACTCATTACTCGTTAAACTCGTT
40359 ACTCATTA
1 ACTCATTA
40367 AGCTCAATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (23 bp):
ACTCATTACTCGTTAAACTCGTT
Found at i:40360 original size:16 final size:16
Alignment explanation
Indices: 40336--40381 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
40326 TAAACTCGTT
40336 ACTCATTACTCGTTAA
1 ACTCATTACTCGTTAA
* *
40352 ACTCGTTACTCATTAA
1 ACTCATTACTCGTTAA
* *
40368 GCTCAATACTCGTT
1 ACTCATTACTCGTT
40382 GCTCGTTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (16 bp):
ACTCATTACTCGTTAA
Found at i:40378 original size:23 final size:23
Alignment explanation
Indices: 40327--40390 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
40317 ATTGCTCGTT
** *
40327 AAACTCGTTACTCATTACTCGTT
1 AAACTCGTTACTCATTAAGCGTC
40350 AAACTCGTTACTCATTAAGC-TC
1 AAACTCGTTACTCATTAAGCGTC
* *
40372 AATACTCGTTGCTCGTTAA
1 AA-ACTCGTTACTCATTAA
40391 ATTCACTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.09
23 32 0.91
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (23 bp):
AAACTCGTTACTCATTAAGCGTC
Found at i:40920 original size:60 final size:59
Alignment explanation
Indices: 40798--40924 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 59
40788 AACATAATGA
* * * **
40798 ATAGTCGGTGACTATTTTATAACTTTTAATAATTGAATGACTTAACAAAGCAACATTTT
1 ATAGTCGATGACTATTTTATAACTTTTAATAATCGAATGACTTAACAAAACAACATCCT
* * *
40857 ATAGTCAGATGACTATTTTATAACTTTTAATAGTCG-ATGGACTTAATAAAACAATATCCT
1 ATAGTC-GATGACTATTTTATAACTTTTAATAATCGAAT-GACTTAACAAAACAACATCCT
40917 ATAGTCGA
1 ATAGTCGA
40925 GTGTATAGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 10 0.17
60 48 0.83
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (59 bp):
ATAGTCGATGACTATTTTATAACTTTTAATAATCGAATGACTTAACAAAACAACATCCT
Found at i:40966 original size:2 final size:2
Alignment explanation
Indices: 40955--41323 Score: 107
Period size: 2 Copynumber: 198.5 Consensus size: 2
40945 GATACCTTTT
*
40955 TA TA -A TA TA TA TA TA TA TA TA T- TA TA TA T- TG TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
40993 TA -A TA T- TA TA T- TA TA TA GTA TA TG T- TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
41031 TA TA T- TA TA TT TG T- TA T- TT TA TG TGG TA TA TA -A TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
* *
41070 T- TA TA TA TT TA TA T- TA TA TA GCA TA TA T- TA TA -A TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * ** *
41108 TA TCA TA TA TA -A TA TA GCA TA TG T- TT TA T- TA CG T- TA TA GA
1 TA T-A TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
41148 TA T- TA TA TA GTA CA TA TA TA TA TT TA TA TA -A TA CA TA GTA T-
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
41189 TA TG TA TA GTA TA TA TA T- TA TA TA T- TA TA CT- TA TT TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
41230 T- TA TA TT TA TA -A TA GTA T- TA TT TA TG TA TA -A CA TA TA T-
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
41268 TA TA -A TA T- TA TA TA TA T- TA TC T- TA TA CGA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
41306 TA GTA TA TA T- TA T- TA TA T
1 TA -TA TA TA TA TA TA TA TA T
41324 TGTATTATTA
Statistics
Matches: 273, Mismatches: 42, Indels: 104
0.65 0.10 0.25
Matches are distributed among these distances:
1 40 0.15
2 213 0.78
3 20 0.07
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41002 original size:27 final size:27
Alignment explanation
Indices: 40961--41123 Score: 100
Period size: 27 Copynumber: 6.0 Consensus size: 27
40951 TTTTTATAAT
*
40961 ATATATATATATATATTATATATTGTATA
1 ATATA-ATAT-TATATTATATATTATATA
* *
40990 ATATAATATTATATTATATAGTATATG
1 ATATAATATTATATTATATATTATATA
*
41017 TTATAATA-TATA-TATATATTATAT-
1 ATATAATATTATATTATATATTATATA
* * * * * ** *
41041 TTGTTATTTTATGTGGTATATAATATA
1 ATATAATATTATATTATATATTATATA
**
41068 CAT-TATATATTTATATTATATAGCATATA
1 -ATATA-ATA-TTATATTATATATTATATA
* * *
41097 TTATAATATTATATCATATATAATATA
1 ATATAATATTATATTATATATTATATA
41124 GCATATGTTT
Statistics
Matches: 103, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
24 5 0.05
25 14 0.14
26 13 0.13
27 39 0.38
28 11 0.11
29 21 0.20
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (27 bp):
ATATAATATTATATTATATATTATATA
Found at i:41015 original size:32 final size:30
Alignment explanation
Indices: 40954--41348 Score: 110
Period size: 31 Copynumber: 12.7 Consensus size: 30
40944 CGATACCTTT
40954 TTATAATATATA-TATATATATATTATATAT-
1 TTATAATATATATTATAT-TATA-TATATATG
40984 TGTATAATATAATATTATATTATATAGTATATG
1 T-TATAATAT-ATATTATATTATATA-TATATG
* * *
41017 TTATAATATATATATATATTATATTTGTTATT
1 TTATAATATATAT-TATATTATATAT-ATATG
** * * *
41049 TTATGTGGTATATAATATACATTATATATTTATA
1 TTA--TAATATAT-AT-TATATTATATATATATG
* *
41083 TTATATAGCATATATTATAATAT-TATATCAT-
1 TTATA-A-TATATATTATATTATATATAT-ATG
* * * *
41114 ATATAATATAGCA-TATGTT-T-TAT-TACG
1 TTATAATATA-TATTATATTATATATATATG
* *
41141 TTATAGATAT-TA-TATAGTACATATATATATT
1 TTATA-ATATATATTATA-T-TATATATATATG
* * *
41172 TATATAATACATAGTATTATGTATAGTATATATA
1 T-TATAATATATATTA-TAT-TATA-TATATATG
41206 TTAT-ATATTATACTTAT-TTATATATTATAT-
1 TTATAATA-TATA-TTATATTATATA-TATATG
* *
41236 TTATAATAGTATTATT-TATGTATA-ACATATA
1 TTATAATA-TA-TATTATAT-TATATATATATG
* *
41267 TTATAATAT-TATATATATTATCT-TATACG
1 TTATAATATATAT-TATATTATATATATATG
* *
41296 ATATATTATATAGTATATATTAT-TATAT-TG
1 TTATAATATATA-T-TATATTATATATATATG
*
41326 -TATTATTATACTATTAATATTAT
1 TTA-TAATATA-TATT-ATATTAT
41349 TCTTGGTTTT
Statistics
Matches: 281, Mismatches: 41, Indels: 86
0.69 0.10 0.21
Matches are distributed among these distances:
26 5 0.02
27 6 0.02
28 11 0.04
29 25 0.09
30 40 0.14
31 70 0.25
32 61 0.22
33 21 0.07
34 29 0.10
35 13 0.05
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (30 bp):
TTATAATATATATTATATTATATATATATG
Found at i:41101 original size:5 final size:5
Alignment explanation
Indices: 40954--41088 Score: 52
Period size: 5 Copynumber: 27.2 Consensus size: 5
40944 CGATACCTTT
* * * *
40954 TTATA ATATA TATATA TATATA TTATATA TTGTA TAATA TAATA TTATA
1 TTATA TTATA T-TATA T-TATA -T-TATA TTATA TTATA TTATA TTATA
* * * *
41003 TTATA -TAGTA -TATG TTATA ATATA -TATA -TATA TTATA TT-TG TTATT
1 TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * *
41049 TTATG TGGTATA TAATA -TACA TTATA -TAT- TTATA TTATA T
1 TTATA T--TATA TTATA TTATA TTATA TTATA TTATA TTATA T
41089 AGCATATATT
Statistics
Matches: 102, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
4 22 0.22
5 59 0.58
6 11 0.11
7 10 0.10
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (5 bp):
TTATA
Found at i:41176 original size:21 final size:21
Alignment explanation
Indices: 41150--41283 Score: 63
Period size: 21 Copynumber: 6.4 Consensus size: 21
41140 GTTATAGATA
41150 TTATATAGTACATA-TATATAT
1 TTATATA-TACATAGTATATAT
41171 TTATATAATACATAGTAT-TAT
1 TTATAT-ATACATAGTATATAT
*
41192 GTATAGTAT--ATA-TAT-TAT
1 TTATA-TATACATAGTATATAT
* * *
41210 ATAT-TATACTTATTTATATAT
1 TTATATATACATA-GTATATAT
*
41231 TATATTTATA-ATAGTAT-TAT
1 T-TATATATACATAGTATATAT
*
41251 TTATGTATAACATA-TATTATAAT
1 TTATATAT-ACATAGTA-TAT-AT
41274 ATTATATATA
1 -TTATATATA
41284 TTATCTTATA
Statistics
Matches: 89, Mismatches: 8, Indels: 30
0.70 0.06 0.24
Matches are distributed among these distances:
16 3 0.03
18 11 0.12
19 9 0.10
20 10 0.11
21 31 0.35
22 11 0.12
23 7 0.08
24 7 0.08
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (21 bp):
TTATATATACATAGTATATAT
Found at i:41303 original size:54 final size:53
Alignment explanation
Indices: 41208--41312 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 53
41198 TATATATATT
* * *
41208 ATATATTATACTTATTTATATATTATATTTATAATAGTATTATTTATGTATAAC
1 ATATATTATACATATTTATATATTATACTTATAATAGTATTATATA-GTATAAC
41262 ATATATTATA-ATATTATATATATTAT-CTTATACGATA-TATTATATAGTATA
1 ATATATTATACATATT-TATATATTATACTTATA--ATAGTATTATATAGTATA
41313 TATTATTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
53 14 0.31
54 28 0.62
55 3 0.07
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (53 bp):
ATATATTATACATATTTATATATTATACTTATAATAGTATTATATAGTATAAC
Found at i:41328 original size:17 final size:17
Alignment explanation
Indices: 41262--41334 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
41252 TATGTATAAC
* *
41262 ATATATTATAATATTAT
1 ATATATTATTATATTGT
*
41279 ATATATTATCT-TATACG-
1 ATATATTAT-TATAT-TGT
41296 ATATATTA-TATA--GT
1 ATATATTATTATATTGT
41310 ATATATTATTATATTGT
1 ATATATTATTATATTGT
41327 AT-TATTAT
1 ATATATTAT
41335 ACTATTAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 5 0.11
16 8 0.17
17 24 0.52
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (17 bp):
ATATATTATTATATTGT
Found at i:51498 original size:32 final size:32
Alignment explanation
Indices: 51409--51507 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 32
51399 TAAGGTGACC
* * *
51409 TTGGGTAGGCTCTAAGGCCCCAAGGCATTTCA
1 TTGGGTAGGCTCTAAGGCCTCAAGGTACTTCA
* * * *
51441 TTGGGTAAGATCTAAGTCCTCAAGGTACTTCT
1 TTGGGTAGGCTCTAAGGCCTCAAGGTACTTCA
* * *
51473 TTGGGTAGGCTCTTAGGCCTTAAGGTACTACA
1 TTGGGTAGGCTCTAAGGCCTCAAGGTACTTCA
51505 TTG
1 TTG
51508 AGTAAGCTAT
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (32 bp):
TTGGGTAGGCTCTAAGGCCTCAAGGTACTTCA
Found at i:52154 original size:31 final size:32
Alignment explanation
Indices: 52093--52155 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
52083 TGGATATTGT
*
52093 TGAATTCTATTTTTAATGTATAAATAATTTTA
1 TGAATTCTATTTTTAATCTATAAATAATTTTA
*
52125 TGAATT-TATATTTT-ATCTATAAATTATTTTA
1 TGAATTCTAT-TTTTAATCTATAAATAATTTTA
52156 CATTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.56
Consensus pattern (32 bp):
TGAATTCTATTTTTAATCTATAAATAATTTTA
Found at i:53231 original size:13 final size:13
Alignment explanation
Indices: 53215--53245 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
53205 AATAAAAATT
53215 ATAAATTTATTTA
1 ATAAATTTATTTA
53228 ATAAATTTATTTA
1 ATAAATTTATTTA
53241 ATAAA
1 ATAAA
53246 AAATTAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAAATTTATTTA
Found at i:55416 original size:23 final size:24
Alignment explanation
Indices: 55380--55424 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
55370 GATTAAATGT
55380 AAATTAATATAGTTTAATTTATAC
1 AAATTAATATAGTTTAATTTATAC
55404 AAATT-ATATAGTTTAATTTAT
1 AAATTAATATAGTTTAATTTAT
55425 GTAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAC
Found at i:58158 original size:15 final size:15
Alignment explanation
Indices: 58138--58166 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58128 TGCTACCGAT
58138 ATTTGACCTGGACTG
1 ATTTGACCTGGACTG
58153 ATTTGACCTGGACT
1 ATTTGACCTGGACT
58167 TGACCTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (15 bp):
ATTTGACCTGGACTG
Found at i:61529 original size:38 final size:39
Alignment explanation
Indices: 61444--61539 Score: 122
Period size: 39 Copynumber: 2.5 Consensus size: 39
61434 TTCAATCCAC
* * * *
61444 CGATTTATTTTCTTTTGCAAAATAGGAAAATAAATCTAA
1 CGATTTATTTCCTTTTACAAAATAGAAAAATAAATCGAA
* *
61483 CAAGTTATTTCCTTTTACAAAATAGAAAAAT-AATCGAA
1 CGATTTATTTCCTTTTACAAAATAGAAAAATAAATCGAA
*
61521 TGATTTATTTCCTTTTACA
1 CGATTTATTTCCTTTTACA
61540 TATCAGAATC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
38 22 0.46
39 26 0.54
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (39 bp):
CGATTTATTTCCTTTTACAAAATAGAAAAATAAATCGAA
Found at i:61678 original size:94 final size:96
Alignment explanation
Indices: 61487--61706 Score: 259
Period size: 94 Copynumber: 2.3 Consensus size: 96
61477 ATCTAACAAG
*
61487 TTATTTCCTTTTACAAAATA-GAAAAATAATCGAATGATTTATTTCCTTTTACATATCAGAATCA
1 TTATTTCCTTTTACAAAATAGGAAAAA-AATCGAATGATTTATTTCCTTTTACAAATCAGAATCA
** * ** ****
61551 TATAAGATTCTTATGAAAATTGATTTTCCGAT
65 TATAAGATTCACAGGAAAATAAATTCAAAGAT
* * * *
61583 TTATTTCATTTTTCAAAATAGGAAAAAAA-C-TATGATTTATTTCTTTTTACAAA-CTAGAATCA
1 TTATTTCCTTTTACAAAATAGGAAAAAAATCGAATGATTTATTTCCTTTTACAAATC-AGAATCA
*
61645 TATAAGATTCACAGGAAAGTAAATTCAAAGAT
65 TATAAGATTCACAGGAAAATAAATTCAAAGAT
61677 TTATTTCCTTTTACAAAATAGGAAAAAAAT
1 TTATTTCCTTTTACAAAATAGGAAAAAAAT
61707 ATACCGATTT
Statistics
Matches: 104, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
93 1 0.01
94 76 0.73
95 1 0.01
96 20 0.19
97 6 0.06
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (96 bp):
TTATTTCCTTTTACAAAATAGGAAAAAAATCGAATGATTTATTTCCTTTTACAAATCAGAATCAT
ATAAGATTCACAGGAAAATAAATTCAAAGAT
Found at i:61717 original size:38 final size:37
Alignment explanation
Indices: 61674--61809 Score: 123
Period size: 39 Copynumber: 3.5 Consensus size: 37
61664 TAAATTCAAA
61674 GATTTATTTCCTTTTACAAAATAGGAAAA-AAATATACC
1 GATTTATTTCCTTTTACAAAATAGGAAAACAAATA-A-C
* * * * * *
61712 GATTTATTTGCTTTCATAAAACAGGAAAACAAACCCAAT
1 GATTTATTTCCTTTTACAAAATAGGAAAACAAA--TAAC
*
61751 GATTTATTTCCTTTTACAAAAT-GTGAAAATGAAATCAAC
1 GATTTATTTCCTTTTACAAAATAG-GAAAA-CAAAT-AAC
*
61790 AATTTATTTCCTTTTACAAA
1 GATTTATTTCCTTTTACAAA
61810 TTAGAATCAT
Statistics
Matches: 78, Mismatches: 14, Indels: 11
0.76 0.14 0.11
Matches are distributed among these distances:
38 26 0.33
39 47 0.60
40 4 0.05
41 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (37 bp):
GATTTATTTCCTTTTACAAAATAGGAAAACAAATAAC
Found at i:61878 original size:40 final size:40
Alignment explanation
Indices: 61834--61921 Score: 115
Period size: 39 Copynumber: 2.2 Consensus size: 40
61824 GATTCTTACA
* * * * * *
61834 AAAATAAATTTTAACAATTTATTTTCTTTTGCAAGATATG
1 AAAATAAATTTCAACAACTTATTTCCTTTTACAAAATAGG
61874 AAAATAAA-TTCAACAACTTATTTCCTTTTACAAAATAGG
1 AAAATAAATTTCAACAACTTATTTCCTTTTACAAAATAGG
61913 AAAATAAAT
1 AAAATAAAT
61922 ACTATGATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 33 0.80
40 8 0.20
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.38
Consensus pattern (40 bp):
AAAATAAATTTCAACAACTTATTTCCTTTTACAAAATAGG
Found at i:62211 original size:57 final size:58
Alignment explanation
Indices: 62135--62322 Score: 238
Period size: 58 Copynumber: 3.2 Consensus size: 58
62125 TAAATGATAA
* * * * * * *
62135 AATCATCCACGATTCTCAAGAAAATAAATTCGATAATTTATTTT-CTTACAAAGTTAG
1 AATCATTCAAGATTTTCAAGGAAATAAATTCAACAATCTATTTTACTTACAAAGTTAG
62192 AATCATTCAAGATTTTCAAGGAAATAAATTCAACAATCTATTTTACTTACAAAGTTAG
1 AATCATTCAAGATTTTCAAGGAAATAAATTCAACAATCTATTTTACTTACAAAGTTAG
* *
62250 AATCA-TCTAAGATTCTT-AAGGAAATAAATTTAACAATCTATTTTCCTTACAAAGTTAG
1 AATCATTC-AAGATT-TTCAAGGAAATAAATTCAACAATCTATTTTACTTACAAAGTTAG
*
62308 AATCAGTGCAAGATT
1 AATCA-TTCAAGATT
62323 CTAAAAATAA
Statistics
Matches: 116, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
57 39 0.34
58 68 0.59
59 8 0.07
60 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (58 bp):
AATCATTCAAGATTTTCAAGGAAATAAATTCAACAATCTATTTTACTTACAAAGTTAG
Found at i:62631 original size:45 final size:45
Alignment explanation
Indices: 62491--62623 Score: 142
Period size: 45 Copynumber: 3.0 Consensus size: 45
62481 TTAGCAACCA
* * * * * * **
62491 AATAATTAAAGGGAATTAATCATTTGATTTTAATCTACACAATC-C
1 AATAATCAAAAGGAACTAATAATTTGATTTTACTTTTGACAA-CAC
* * *
62536 AATAATCGAAAGGAACTAATCATTTGATTTTACTTTTGGCAACAC
1 AATAATCAAAAGGAACTAATAATTTGATTTTACTTTTGACAACAC
*
62581 AATAATCAAAATGAACTAATAATTTGATTTTACTTTTGACAAC
1 AATAATCAAAAGGAACTAATAATTTGATTTTACTTTTGACAAC
62624 CCGATAATTA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 1 0.01
45 73 0.99
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (45 bp):
AATAATCAAAAGGAACTAATAATTTGATTTTACTTTTGACAACAC
Found at i:62779 original size:22 final size:19
Alignment explanation
Indices: 62736--62787 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
62726 AAACACAATC
62736 AATAATTATTATAATATTT
1 AATAATTATTATAATATTT
62755 AATAATTATTATAATATTT
1 AATAATTATTATAATATTT
*
62774 AATAATAATTATAA
1 AATAATTATTATAA
62788 ACACCAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATTATTATAATATTT
Found at i:64507 original size:77 final size:76
Alignment explanation
Indices: 64418--64567 Score: 264
Period size: 76 Copynumber: 2.0 Consensus size: 76
64408 TTCATTGTAC
*
64418 AAAAAAATTTGAGATGAACGTGAACTAAAATAAAAAATATTTATTTAAATTTACAATACTTCCAA
1 AAAAAAATTTGAGATAAACGTGAACTAAAAT-AAAAATATTTATTTAAATTTACAATACTTCCAA
64483 CTTATAAAAATA
65 CTTATAAAAATA
* *
64495 AAAAAAATTTGAGATAAACGTGAATTAAAATAAAGATATTTATTTAAATTTACAATACTTCCAAC
1 AAAAAAATTTGAGATAAACGTGAACTAAAATAAAAATATTTATTTAAATTTACAATACTTCCAAC
64560 TTATAAAA
66 TTATAAAA
64568 TAATGTAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
76 41 0.59
77 29 0.41
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.32
Consensus pattern (76 bp):
AAAAAAATTTGAGATAAACGTGAACTAAAATAAAAATATTTATTTAAATTTACAATACTTCCAAC
TTATAAAAATA
Found at i:77080 original size:41 final size:41
Alignment explanation
Indices: 77026--77336 Score: 274
Period size: 41 Copynumber: 7.6 Consensus size: 41
77016 AATCGATTTA
* * * *
77026 GATCTTGGCAGCATGCAACAGTTCATCATTCAACTTGATTC
1 GATCATGGCAGCATACAATAATTCATCATTCAACTTGATTC
* * * * *
77067 GATCATGGTAGCATACAAACAATTCACCATTCGA-TCTAATTC
1 GATCATGGCAGCATAC-AATAATTCATCATTCAACT-TGATTC
* *
77109 -ATCATGGCAGCATACCATATTTCATCATTCAACTTGATT-
1 GATCATGGCAGCATACAATAATTCATCATTCAACTTGATTC
* * * * *
77148 GATTATGGTAGCATGCAATAATTCACCATTCAA-TTCAATTC
1 GATCATGGCAGCATACAATAATTCATCATTCAACTT-GATTC
* *
77189 -ATCATGGCAGCATACAATAATCCATCATTCAACTTGATTT
1 GATCATGGCAGCATACAATAATTCATCATTCAACTTGATTC
* * *
77229 GATCATGGTAGCATGCAATAATTCATCATTCAA-TTCAATTC
1 GATCATGGCAGCATACAATAATTCATCATTCAACTT-GATTC
* * * *
77270 AATCATGGCAGCATACAATACTTCACCATTCAACCTGATTC
1 GATCATGGCAGCATACAATAATTCATCATTCAACTTGATTC
* * * * *
77311 AACCACGGTAGCATACCATAATTCAT
1 GATCATGGCAGCATACAATAATTCAT
77337 TCAACTTGAC
Statistics
Matches: 214, Mismatches: 46, Indels: 20
0.76 0.16 0.07
Matches are distributed among these distances:
39 2 0.01
40 77 0.36
41 115 0.54
42 20 0.09
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (41 bp):
GATCATGGCAGCATACAATAATTCATCATTCAACTTGATTC
Found at i:77336 original size:82 final size:81
Alignment explanation
Indices: 77031--77335 Score: 389
Period size: 82 Copynumber: 3.8 Consensus size: 81
77021 ATTTAGATCT
* * * *
77031 TGGCAGCATGCAACAGTTCATCATTCAACTTGATTCGATCATGGTAGCATACAAACAATTCACCA
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTCGATCATGGTAGCATAC-AATAATTCACCA
*
77096 TTCGA-TCTAATTCATCA
65 TTCAATTC-AATTCATCA
* * * *
77113 TGGCAGCATACCATATTTCATCATTCAACTTGATT-GATTATGGTAGCATGCAATAATTCACCAT
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTCGATCATGGTAGCATACAATAATTCACCAT
77177 TCAATTCAATTCATCA
66 TCAATTCAATTCATCA
* * * *
77193 TGGCAGCATACAATAATCCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTCGATCATGGTAGCATACAATAATTCACCAT
77258 TCAATTCAATTCAATCA
66 TCAATTCAATTC-ATCA
* * * * * * *
77275 TGGCAGCATACAATACTTCACCATTCAACCTGATTCAACCACGGTAGCATACCATAATTCA
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTCGATCATGGTAGCATACAATAATTCA
77336 TTCAACTTGA
Statistics
Matches: 197, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
80 56 0.28
81 55 0.28
82 86 0.44
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.31
Consensus pattern (81 bp):
TGGCAGCATACAATAATTCATCATTCAACTTGATTCGATCATGGTAGCATACAATAATTCACCAT
TCAATTCAATTCATCA
Found at i:78718 original size:21 final size:21
Alignment explanation
Indices: 78694--78733 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
78684 GCGTAGAATT
78694 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
78715 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
78734 AAACACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.15
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:78763 original size:17 final size:18
Alignment explanation
Indices: 78736--78779 Score: 72
Period size: 17 Copynumber: 2.4 Consensus size: 18
78726 ACCACATAAA
78736 ACACATATGTCCCGAAGG
1 ACACATATGTCCCGAAGG
78754 ACAC-TATGTCCCGAAGG
1 ACACATATGTCCCGAAGG
78771 ACCACATAT
1 A-CACATAT
78780 ACACATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.58
18 7 0.29
19 3 0.12
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.18
Consensus pattern (18 bp):
ACACATATGTCCCGAAGG
Found at i:78771 original size:45 final size:45
Alignment explanation
Indices: 78694--78813 Score: 161
Period size: 45 Copynumber: 2.6 Consensus size: 45
78684 GCGTAGAATT
78694 TGTCCCGAAGGACCACATAGATGTCCCGAAGGACCACATAAAACACATA
1 TGTCCCGAAGGACCAC-T--ATGTCCCGAAGGACCACAT-AAACACATA
*
78743 TGTCCCGAAGGA-CACTATGTCCCGAAGGACCACATATACACATA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACATAAACACATA
* * *
78787 TATCCCGAAAGACCACTATGTTCCGAA
1 TGTCCCGAAGGACCACTATGTCCCGAA
78814 TGACGCGTAG
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
44 18 0.27
45 32 0.48
47 1 0.02
48 3 0.05
49 12 0.18
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.17
Consensus pattern (45 bp):
TGTCCCGAAGGACCACTATGTCCCGAAGGACCACATAAACACATA
Done.